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root/OpenMD/trunk/src/io/Globals.cpp

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stdlib.h>
#	Line 49 | Line 50
50		#include "utils/MemoryUtils.hpp"
51		#include "utils/simError.h"
52
53	<	namespace oopse {
54	<	Globals::Globals() {
54	<	DefineParameter(ForceField, "forceField")
55	<
56	<	DefineOptionalParameter(TargetTemp, "targetTemp");
57	<	DefineOptionalParameter(Ensemble, "ensemble");
58	<	DefineOptionalParameter(Dt, "dt");
59	<	DefineOptionalParameter(RunTime, "runTime");
60	<	DefineOptionalParameter(FinalConfig, "finalConfig");
61	<	DefineOptionalParameter(SampleTime, "sampleTime");
62	<	DefineOptionalParameter(ResetTime, "resetTime");
63	<	DefineOptionalParameter(StatusTime, "statusTime");
64	<	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65	<	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66	<	DefineOptionalParameter(TempSet, "tempSet");
67	<	DefineOptionalParameter(ThermalTime, "thermalTime");
68	<	DefineOptionalParameter(TargetPressure, "targetPressure");
69	<	DefineOptionalParameter(TauThermostat, "tauThermostat");
70	<	DefineOptionalParameter(TauBarostat, "tauBarostat");
71	<	DefineOptionalParameter(ZconsTime, "zconsTime");
72	<	DefineOptionalParameter(ZconsTol, "zconsTol");
73	<	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74	<	DefineOptionalParameter(Seed, "seed");
75	<	DefineOptionalParameter(Minimizer, "minimizer");
76	<	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78	<	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79	<	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80	<	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81	<	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82	<	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
83	<	DefineOptionalParameter(ZconsGap, "zconsGap");
84	<	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
85	<	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
86	<	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
87	<	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88	<	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89	<	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	<	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94	<	DefineOptionalParameter(SurfaceTension, "surfaceTension");
95	<	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96	<	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97	<	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99	<	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100	<	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101	<	DefineOptionalParameter(Viscosity, "viscosity");
102	<	DefineOptionalParameter(BeadSize, "beadSize");
103	<	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104	<	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105	<	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
53	>	namespace OpenMD {
54	>	Globals::Globals() {
55
56	<
57	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
58	<	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
110	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
111	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
112	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
113	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
114	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
115	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
116	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
117	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
118	<	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
119	<	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120	<	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
121	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
122	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
123	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
124	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
125	<	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
126	<	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
56	>	flucQpars_ = new FluctuatingChargeParameters();
57	>	rnemdPars_ = new RNEMDParameters();
58	>	minimizerPars_ = new MinimizerParameters();
59
60	<	deprecatedKeywords_.insert("nComponents");
129	<	deprecatedKeywords_.insert("nZconstraints");
130	<	deprecatedKeywords_.insert("initialConfig");
60	>	DefineParameter(ForceField, "forceField");
61
62	<	}
62	>	DefineOptionalParameter(TargetTemp, "targetTemp");
63	>	DefineOptionalParameter(Ensemble, "ensemble");
64	>	DefineOptionalParameter(Dt, "dt");
65	>	DefineOptionalParameter(RunTime, "runTime");
66	>	DefineOptionalParameter(FinalConfig, "finalConfig");
67	>	DefineOptionalParameter(SampleTime, "sampleTime");
68	>	DefineOptionalParameter(ResetTime, "resetTime");
69	>	DefineOptionalParameter(StatusTime, "statusTime");
70	>	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71	>	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
72	>	DefineOptionalParameter(TempSet, "tempSet");
73	>	DefineOptionalParameter(ThermalTime, "thermalTime");
74	>	DefineOptionalParameter(TargetPressure, "targetPressure");
75	>	DefineOptionalParameter(TauThermostat, "tauThermostat");
76	>	DefineOptionalParameter(TauBarostat, "tauBarostat");
77	>	DefineOptionalParameter(ZconsTime, "zconsTime");
78	>	DefineOptionalParameter(ZconsTol, "zconsTol");
79	>	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80	>	DefineOptionalParameter(Seed, "seed");
81	>	DefineOptionalParameter(ZconsGap, "zconsGap");
82	>	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83	>	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
84	>	DefineOptionalParameter(ThermodynamicIntegrationLambda,
85	>	"thermodynamicIntegrationLambda");
86	>	DefineOptionalParameter(ThermodynamicIntegrationK,
87	>	"thermodynamicIntegrationK");
88	>	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89	>	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	>	DefineOptionalParameter(SurfaceTension, "surfaceTension");
92	>	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93	>	DefineOptionalParameter(ElectricField, "electricField");
94
95	<	Globals::~Globals() {
96	<	MemoryUtils::deletePointers(components_);
97	<	MemoryUtils::deletePointers(zconstraints_);
98	<	}
95	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
96	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
97	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99	>	DefineOptionalParameter(Viscosity, "viscosity");
100	>	DefineOptionalParameter(BeadSize, "beadSize");
101	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
104	>	DefineOptionalParameter(UseMultipleTemperatureMethod,
105	>	"useMultipleTemperatureMethod");
106	>	DefineOptionalParameter(ElectrostaticSummationMethod,
107	>	"electrostaticSummationMethod");
108	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
109	>	DefineOptionalParameter(MTM_G, "MTM_G");
110	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
111	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
112	>	DefineOptionalParameter(MTM_R, "MTM_R");
113	>	DefineOptionalParameter(Alpha, "alpha");
114	>	DefineOptionalParameter(ConstraintTime, "constraintTime");
115
116	<	void Globals::validate() {
117	<	DataHolder::validate();
118	<
119	<	CheckParameter(ForceField, isNotEmpty());
120	<	CheckParameter(TargetTemp, isPositive());
121	<	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
122	<	CheckParameter(Dt, isPositive());
123	<	CheckParameter(RunTime, isPositive());
124	<	CheckParameter(FinalConfig, isNotEmpty());
125	<	CheckParameter(SampleTime, isNonNegative());
126	<	CheckParameter(ResetTime, isNonNegative());
127	<	CheckParameter(StatusTime, isNonNegative());
128	<	CheckParameter(CutoffRadius, isPositive());
129	<	CheckParameter(SwitchingRadius, isNonNegative());
130	<	CheckParameter(Dielectric, isPositive());
131	<	CheckParameter(ThermalTime,  isNonNegative());
132	<	CheckParameter(TauThermostat, isPositive());
133	<	CheckParameter(TauBarostat, isPositive());
134	<	CheckParameter(ZconsTime, isPositive());
135	<	CheckParameter(ZconsTol, isPositive());
136	<	CheckParameter(Seed, isPositive());
137	<	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
138	<	CheckParameter(MinimizerMaxIter, isPositive());
139	<	CheckParameter(MinimizerWriteFrq, isPositive());
140	<	CheckParameter(MinimizerStepSize, isPositive());
141	<	CheckParameter(MinimizerFTol, isPositive());
142	<	CheckParameter(MinimizerGTol, isPositive());
143	<	CheckParameter(MinimizerLSTol, isPositive());
144	<	CheckParameter(MinimizerLSMaxIter, isPositive());
145	<	CheckParameter(ZconsGap, isPositive());
146	<	CheckParameter(ZconsFixtime, isPositive());
147	<	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
148	<	CheckParameter(ThermodynamicIntegrationK, isPositive());
149	<	CheckParameter(ForceFieldVariant, isNotEmpty());
150	<	CheckParameter(ForceFieldFileName, isNotEmpty());
151	<	CheckParameter(ThermIntDistSpringConst, isPositive());
152	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
153	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
154	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
155	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
156	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
157	<	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
158	<	//CheckParameter(StatFileFormat,);
159	<	CheckParameter(OrthoBoxTolerance, isPositive());
160	<	CheckParameter(ThermIntDistSpringConst, isPositive());
161	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
162	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
163	<	CheckParameter(DampingAlpha,isNonNegative());
164	<	CheckParameter(SkinThickness, isPositive());
165	<	CheckParameter(Viscosity, isNonNegative());
166	<	CheckParameter(BeadSize, isPositive());
167	<	CheckParameter(FrozenBufferRadius, isPositive());
168	<	CheckParameter(LangevinBufferRadius, isPositive());
169	<	CheckParameter(NeighborListNeighbors, isPositive());
170	<
171	<	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
172	<	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
116	>
117	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
118	>	"usePeriodicBoundaryConditions",
119	>	true);
120	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
121	>	true);
122	>	DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
123	>	"useLongRangeCorrections", true);
124	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
125	>	false);
126	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
127	>	"useInitialExtendedSystemState",
128	>	false);
129	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
130	>	"orthoBoxTolerance", 1E-6);
131	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
132	>	"SHIFTED_FORCE");
133	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
134	>	"electrostaticScreeningMethod",
135	>	"DAMPED");
136	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
137	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile,
138	>	"compressDumpFile", false);
139	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
140	>	false);
141	>	DefineOptionalParameterWithDefaultValue(OutputForceVector,
142	>	"outputForceVector", false);
143	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
144	>	"outputParticlePotential", false);
145	>	DefineOptionalParameterWithDefaultValue(OutputElectricField,
146	>	"outputElectricField", false);
147	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
148	>	"outputFluctuatingCharges", false);
149	>	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
150	>	"outputSitePotential", false);
151	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
152	>	1.0);
153	>	DefineOptionalParameterWithDefaultValue(StatFileFormat,
154	>	"statFileFormat",
155	>	"TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
156	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
157	>	"useSphericalBoundaryConditions",
158	>	false);
159	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
160	>	"accumulateBoxDipole", false);
161	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
162	>	false);
163	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
164	>	"idealCrystal.in");
165	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
166	>	"useThermodynamicIntegration",
167	>	false);
168	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
169	>
170	>	deprecatedKeywords_.insert("nComponents");
171	>	deprecatedKeywords_.insert("nZconstraints");
172	>	deprecatedKeywords_.insert("initialConfig");
173	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
174	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
175	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
176	>	deprecatedKeywords_.insert("useSolidThermInt");
177	>	deprecatedKeywords_.insert("useLiquidThermInt");
178	>	deprecatedKeywords_.insert("minimizerMaxIter");
179	>	deprecatedKeywords_.insert("minimizerWriteFreq");
180	>	deprecatedKeywords_.insert("minimizerStepSize");
181	>	deprecatedKeywords_.insert("minimizerFTol");
182	>	deprecatedKeywords_.insert("minimizerGTol");
183	>	deprecatedKeywords_.insert("minimizerLSTol");
184	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
185	>
186	>
187	>	}
188	>
189	>	Globals::~Globals() {
190	>	MemoryUtils::deletePointers(components_);
191	>	MemoryUtils::deletePointers(zconstraints_);
192	>	MemoryUtils::deletePointers(restraints_);
193	>	delete flucQpars_;
194	>	delete rnemdPars_;
195	>	delete minimizerPars_;
196	>	}
197	>
198	>	void Globals::validate() {
199	>	DataHolder::validate();
200	>
201	>	CheckParameter(ForceField, isNotEmpty());
202	>	CheckParameter(TargetTemp, isPositive());
203	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
204	>	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
205	>	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
206	>	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
207	>	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
208	>	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
209	>	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
210	>	isEqualIgnoreCase("NGT") ||
211	>	isEqualIgnoreCase("LANGEVINHULL") ||
212	>	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
213	>	CheckParameter(Dt, isPositive());
214	>	CheckParameter(RunTime, isPositive());
215	>	CheckParameter(FinalConfig, isNotEmpty());
216	>	CheckParameter(SampleTime, isNonNegative());
217	>	CheckParameter(ResetTime, isNonNegative());
218	>	CheckParameter(StatusTime, isNonNegative());
219	>	CheckParameter(CutoffRadius, isPositive());
220	>	CheckParameter(SwitchingRadius, isNonNegative());
221	>	CheckParameter(Dielectric, isPositive());
222	>	CheckParameter(ThermalTime,  isNonNegative());
223	>	CheckParameter(TauThermostat, isPositive());
224	>	CheckParameter(TauBarostat, isPositive());
225	>	CheckParameter(ZconsTime, isPositive());
226	>	CheckParameter(ZconsTol, isPositive());
227	>	CheckParameter(Seed, isPositive());
228	>	CheckParameter(ZconsGap, isPositive());
229	>	CheckParameter(ZconsFixtime, isPositive());
230	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
231	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
232	>	CheckParameter(ForceFieldVariant, isNotEmpty());
233	>	CheckParameter(ForceFieldFileName, isNotEmpty());
234	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
235	>	isEqualIgnoreCase("SWITCHED") ||
236	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
237	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
238	>	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
239	>	isEqualIgnoreCase("EWALD_FULL"));
240	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
241	>	isEqualIgnoreCase("MAX") ||
242	>	isEqualIgnoreCase("TRADITIONAL"));
243	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
244	>	isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
245	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
246	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
247	>	isEqualIgnoreCase("REACTION_FIELD") ||
248	>	isEqualIgnoreCase("TAYLOR_SHIFTED"));
249	>	CheckParameter(ElectrostaticScreeningMethod,
250	>	isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
251	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
252	>	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
253	>	CheckParameter(OrthoBoxTolerance, isPositive());
254	>	CheckParameter(DampingAlpha,isNonNegative());
255	>	CheckParameter(SkinThickness, isPositive());
256	>	CheckParameter(Viscosity, isNonNegative());
257	>	CheckParameter(BeadSize, isPositive());
258	>	CheckParameter(FrozenBufferRadius, isPositive());
259	>	CheckParameter(LangevinBufferRadius, isPositive());
260	>	CheckParameter(NeighborListNeighbors, isPositive());
261	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
262	>	isEqualIgnoreCase("AlphaShape"));
263	>	CheckParameter(Alpha, isPositive());
264	>
265	>	for(std::vector<Component*>::iterator i = components_.begin();
266	>	i != components_.end(); ++i) {
267	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
268		std::ostringstream oss;
269	<	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
270	<	throw OOPSEException(oss.str());
269	>	oss << "Globals Error: can not find molecule stamp for component "
270	>	<< (*i)->getType() << std::endl;
271	>	throw OpenMDException(oss.str());
272	>	}
273		}
274		}
275	<	}
276	<
203	<	bool Globals::addComponent(Component* comp) {
275	>
276	>	bool Globals::addComponent(Component* comp) {
277		components_.push_back(comp);
278		return true;
279	<	}
279	>	}
280
281	<	bool Globals::addZConsStamp(ZConsStamp* zcons) {
281	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
282		zconstraints_.push_back(zcons);
283		return true;
284	<	}
284	>	}
285
286	<	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
286	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
287	>	restraints_.push_back(rest);
288	>	return true;
289	>	}
290	>
291	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
292	>	if (flucQpars_ != NULL)
293	>	delete flucQpars_;
294	>
295	>	flucQpars_ = fqp;
296	>	return true;
297	>	}
298	>
299	>	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
300	>	if (rnemdPars_ != NULL)
301	>	delete rnemdPars_;
302	>
303	>	rnemdPars_ = rnemdPars;
304	>	return true;
305	>	}
306	>
307	>	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
308	>	if (minimizerPars_ != NULL)
309	>	delete minimizerPars_;
310	>
311	>	minimizerPars_ = miniPars;
312	>	return true;
313	>	}
314	>
315	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
316		std::string molStampName = molStamp->getName();
317		std::map<std::string, MoleculeStamp*>::iterator i;
318		bool ret = false;
319		i = moleculeStamps_.find(molStampName);
320		if (i == moleculeStamps_.end()) {
321	<	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
322	<	ret = true;
321	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
322	>	ret = true;
323		} else {
324	<	std::ostringstream oss;
325	<	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
326	<	throw OOPSEException(oss.str());
324	>	std::ostringstream oss;
325	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
326	>	<< "appears multiple times\n";
327	>	throw OpenMDException(oss.str());
328		}
329		return ret;
330	+	}
331		}
228	–
229	–
230	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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